Maybe Off Topic, I found an bug (since version 2.0) with Apple Smart Keyboard (maybe same with USB keyboards like Magic Keyboard). Sometimes I wasn"t able to get the "Spacebar". Other keys worked fine. In other apps the "Spacebar" was also available. To reconnect the keyboard wasn't the solution. I have to restart the Pythonisa App. After that, the "Spacebar" was back!

When extended keyboard with numbers is on, alternate keys show as expected on both rows. Only remarks are that top row has pop ups above, 2nd row to the left; and that top row becomes darker when pop ups show. This may be by design.

When extended is off, alternate keys work for the single row (popping up left as before). The exception is for quote, for which the pop up doesn't show (only a small part), but the logic works, i.e. If I swipe left on quote to bracket, I get triple quote.

I'm on:
Pythonista version 2.0.1 (201000) on iOS 9.2 on an iPad5,4 with a screen size of 1024 x 768.

My theory for the differences between the two extra keyboard rows is that the bottom one uses iOS 9's native "extra keyboard row" and the top one is added by Pythonista, meaning that the bottom row's graphics cannot draw outside its bounding box to display the tap-and-hold menus above the keys.